The plots here come from an analysis from Kalucka supplementary data, where the different markers posted have been taken and analysed over the 20-01-2021 Liver scRNASeq experiment. In said experiments there are four different set of Conditions, Control, Dll4KO, RbpjKO and Notch1KO. In said experiment it has been observed that the traditional arterial phenotype is lost in LOF mice, yet mice can still function. Therefore, we hipothesise that Endothelial Cells develop a new kind of arterial phenotype as an emergency mechanism due to lack of proper traditional arterial EC differentiation.
For this reason we set into looking at different markers that have been validated as arterial, venous or capillary phenotypes and look at the spread in the 20-01-21 Liver experiment, with the aim of finding a considerable difference in the spread between the Control and the 3 LOF samples. Ideally we want to localize the cluster where the arterial “emergency” phenotype forms in the LOF samples.
The Kalucka supplementary data separates the data in different set of categories, them being:
The same criteria will be used when showing the plots.
We want to see a clear difference in the arterio-venous differentiation spread of Control vs. LOF (Dll4, Rbpj, Notch1) samples
library("Seurat")
library("openxlsx")
library("knitr")
library("rmarkdown")
library("yaml")
Carlos <- readRDS("SC.Analysis.SecondPass.RNA.Singlets.Endothelial.ManualClustering.seuratSC.Final.V4.rds")
Top50_arterial_capillary
Top50_arterial_capillary_Vln
Conserved_artery
Conserved_vein
There were no remarkable markers in this section (capillary markers tend to be expressed in all cells)